Genomic Science in Understanding Cholera Outbreaks and Evolution of Vibrio cholerae as a Human Pathogen

Abstract

Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTX–ϕ prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core- and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent.

Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017

“…The accessory genome of the analyzed strains essentially constitutes of genomic islands mainly the Vibrio Pathogenicity Islands, toxin co-regulated pilus biosynthesis proteins, the CTX prophage, and resistance genes on the SXT integrative conjugative element (Fig 4). These findings corroborates previous finding [37,39] and confirms that the CTX prophage is not part of the core genome of V . cholerae O1.…”

Sensitivity to Polymyxin B in El TorVibrio choleraeO1 Strain, Kolkata, India

“…Among phenotypic traits distinguishing the 2 biotypes, sensitivity to polymyxin B (50 U) is considered a reliable indicator and stable phenotype for biotyping. Research has shown that the genome of V. cholerae strains is undergoing cryptic changes that influence the strains’ virulence, rapid transmission, and spread ( 4 ). Our previous findings showed El Tor strains with few biotype traits of classical strains ( 5 ).…”

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

“…This aligned the cholera outbreak in Nepal and the arrival of Nepalese soldiers in Haiti with the start of the Haitian outbreak (145). WGS provided particularly strong evidence that Nepalese UN peacekeeping troops brought cholera to Haiti (154)(155)(156). The intricacies of this outbreak could not have been solved and the source of the contamination would not have been conclusively identified without the use of a WGS typing approach.…”